Invalid type of X ValueError lists unclear accepted types (#1395)

* add module info to allowed types

* Update anndata/_core/anndata.py

Co-authored-by: Isaac Virshup <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* added test

* release note and latest discussed msg string

---------

Co-authored-by: Isaac Virshup <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

anndata/_core/anndata.py

@@ -421,9 +421,8 @@ def _init_as_actual(
                 if isinstance(X, s_type.value):
                     break
             else:
-                class_names = ", ".join(c.__name__ for c in StorageType.classes())
                 raise ValueError(
-                    f"`X` needs to be of one of {class_names}, not {type(X)}."
+                    f"X needs to be of one of numpy.ndarray, numpy.ma.core.MaskedArray, scipy.sparse.spmatrix, h5py.Dataset, zarr.Array, anndata.experimental.[CSC,CSR]Dataset, dask.array.Array, cupy.ndarray, cupyx.scipy.sparse.spmatrix, not {type(X)}."
                 )
             if shape is not None:
                 raise ValueError("`shape` needs to be `None` if `X` is not `None`.")

anndata/tests/test_base.py

@@ -89,6 +89,16 @@ def test_creation_error(src, src_arg, dim_msg, dim, dim_arg, msg: str | None):
         AnnData(**{src: src_arg, dim: dim_arg(dim)})
 
 
+def test_invalid_X():
+    with pytest.raises(
+        ValueError,
+        match=re.escape(
+            "X needs to be of one of numpy.ndarray, numpy.ma.core.MaskedArray, scipy.sparse.spmatrix, h5py.Dataset, zarr.Array, anndata.experimental.[CSC,CSR]Dataset, dask.array.Array, cupy.ndarray, cupyx.scipy.sparse.spmatrix, not <class 'str'>."
+        ),
+    ):
+        AnnData("string is not a valid X")
+
+
 def test_create_with_dfs():
     X = np.ones((6, 3))
     obs = pd.DataFrame(dict(cat_anno=pd.Categorical(["a", "a", "a", "a", "b", "a"])))

docs/release-notes/0.10.6.md

@@ -8,6 +8,7 @@
 * Bring optimization from {pr}`1233` to indexing on the whole `AnnData` object, not just the sparse dataset itself {pr}`1365` {user}`ilan-gold`
 * Fix mean slice length checking to use improved performance when indexing backed sparse matrices with boolean masks along their major axis {pr}`1366` {user}`ilan-gold`
 * Fixed overflow occurring when writing dask arrays with sparse chunks by always writing dask arrays with 64 bit indptr and indices, and adding an overflow check to `.append` method of sparse on disk structures {pr}`1348` {user}`ivirshup`
+* Modified `ValueError` message for invalid `.X` during construction to show more helpful list instead of ambiguous `__name__` {pr}`1395` {user}`eroell`
 
 ```{rubric} Documentation
 ```